About

13 Responses

The Zebrafish new assembly (Zv9) has been out (in Ensembl and UCSC) for a while, yet the miRNA tracks in miRBase has not been updated yet. Does anyone has an idea, when the miRNA annotations in Zv9 be released.

I am new to the world of microRNA, and I am trying to figure out all of the rules of nomenclature and understanding the information in the database. Can someone explain what exactly “reads per million” or RPM means? I know it relates to expression of the microRNA, but what exactly is a “read” and how is this calculated?

I just wandered why there are no miRNAs from protozoan parasites deposited in the miRBase. For example, there are papers by Wang C team on Giardia lamblia miRNAs that are validated by Northern blot and other techniques (for example: Li et al, 2012. Cellular Microbiology 14, 1455-1473). Also from Toxoplasma gondii (Braun L et al 2010 Plos Pathogens Volume 6, Issue 5 e1000920. Did you ever received these miRNAs?

We do have a few non-animal, non-plant miRNAs that have been published and submitted to us. The sets we don’t have were not submitted, or it was agreed with authors not to deposit them. There is some controversy in the community about these. This paper for example implies that these sequences are not likely to be miRNAs:

As I understand it, many protozoans (most trypanosomes for example) don’t have the RNAi machinery, so won’t have miRNAs by the current definition. That does not of course mean that they don’t have interesting small RNAs.

Currently the only way to get these data en masse is from the dump of the mysql database. In the database_files directory on the FTP site, there is a file called mirna_context.txt, which is a table of all miRNAs that overlap with Ensembl transcript annotations. The first column links to the file mirna.txt, which has the miRNA name and other info. The other columns of the mirna_context table are: